Well, if you use Buzz droids against a capital ship (or any big ships for that matter) then the aim for the buzz droids is weaken but not destruction.
Simply put, the buzz droids should be set to damage weak installments on the hull. There are spots on a big ship that is weak in armor but really difficult to hit, for example, the laser turrets and cannons and directional thrusters.
Well damaging such systems will not destroy the big ships, but they will reduce their effectiveness, sometimes by critical amounts.
Think of the below cases:
1) Sopme of the turning thrusters are weakened, so CIS ships can get a nice rake shot at its engine.
2) Main laser turrets are damaged, and only function at 50% effeciveness.
3) 30% of Anti-freighter turrets turning error, unable to track targets.
4) Communication towers damaged, command/coordination range reduced.
5) Hanger Door mechanism damaged, allow 3 minutes or repair procedure (which even 5 seconds can mean life and death)
All of the above does not destroy the ship, but can have extreme effect to the battle as a whole.
This is even more effect when you take into account that most giant structures in star wars have small but potentually deadly weak points.